1-11497869-T-G

Variant names:

• chr1-11497869-T-G
• rs4846012
• NM_020780.2:c.-3-3121T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020780.2(DISP3):​c.-3-3121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,162 control chromosomes in the GnomAD database, including 20,551 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (20551 hom., cov: 32)
• Consequence: DISP3 NM_020780.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 5 publications found

Genes affected

DISP3 (HGNC:29251): (dispatched RND transporter family member 3) Involved in negative regulation of neuron differentiation; positive regulation of lipid metabolic process; and positive regulation of neural precursor cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC124903842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020780.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP3	NM_020780.2	MANE Select	c.-3-3121T>G		intron	N/A	NP_065831.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP3	ENST00000294484.7	TSL:1 MANE Select	c.-3-3121T>G		intron	N/A	ENSP00000294484.6

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71589 AN: 152042 Hom.: 20546 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 71601 AN: 152162 Hom.: 20551 Cov.: 32 AF XY: 0.467 AC XY: 34745 AN XY: 74372

African (AFR) AF: 0.142 AC: 5909 AN: 41534

American (AMR) AF: 0.581 AC: 8880 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1384 AN: 5184

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4816

European-Finnish (FIN) AF: 0.630 AC: 6653 AN: 10566

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43427 AN: 67980

Other (OTH) AF: 0.487 AC: 1029 AN: 2112

Alfa AF: 0.572 Hom.: 12269

Bravo AF: 0.458

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.80
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4846012; hg19: chr1-11557926; COSMIC: COSV53823718;